The cyst is normal and probably is from where you ovulated.
As for the progesterone level, mine has only been tested a few times and when it was low I shortly thereafter miscarried. Mine were all tested before I had an ultrasound, though. Lots of women do prometrium so it isn't unusual to use/take it.
Right now your body is producing the progesterone so I'd personally would want to take prometrium because the baby could be fine and you could still miscarry due to low progesterone. Progesterone is what maintains the lining and prevents cramping to shed the lining. Around 12/13 weeks the placenta starts making the progesterone instead and thus the baby starts maintaining his/her cozy temporary home. That is my understanding, at least.